Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) is increasingly utilized as a rapid technique to identify microorganisms including pathogenic bacteria. However, little attention has been paid to the significant proteomic information encoded in the MS peaks that collectively constitute the MS 'fingerprint'. This review/perspective is intended to explore this topic in greater detail in the hopes that it may spur interest and further research in this area. Areas covered: This paper examines the recent literature on utilizing MALDI-TOF for bacterial identification. Critical works highlighting protein biomarker identification of bacteria, arguments for and against protein biomarker identification, proteomic approaches to biomarker identification, emergence of MALDI-TOF-TOF platforms and their use for top-down proteomic identification of bacterial proteins, protein denaturation and its effect on protein ion fragmentation, collision cross-sections and energy deposition during desorption/ionization are also explored. Expert commentary: MALDI-TOF and TOF-TOF mass spectrometry platforms will continue to provide chemical analyses that are rapid, cost-effective and high throughput. These instruments have proven their utility in the taxonomic identification of pathogenic bacteria at the genus and species level and are poised to more fully characterize these microorganisms to the benefit of clinical microbiology, food safety and other fields.